title: mouse65_vs_mixed_sex_pool: brain

source_name: mouse65, brain


title: mouse67_vs_mixed_sex_pool: brain

status: Public on Aug 31 2009

type: RNA

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

hyb_protocol: The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)

scan_protocol: Standard dual-channel Agilent scanner with manufacturer provided software.

data_processing: See Rosetta Error Model (PMID: 16522673)

molecule: polyA RNA

organism: Mus musculus

source_name: mouse67, brain

label_protocol: Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.

growth_protocol: All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.

extract_protocol: Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.

tag: strain

value: CAST/EiJ x C57BL/6J

tag: treatment category

value: test sample

tag: tissue

value: brain

tag: sex

value: female

source_name: reference pool (mixed sex, brain)

value: reference pool

value: mixed


title: mouse63_vs_mixed_sex_pool: brain

source_name: mouse63, brain


title: mouse80_vs_mixed_sex_pool: brain

source_name: mouse80, brain


title: mouse64_vs_mixed_sex_pool: brain

source_name: mouse64, brain

value: male


title: mouse66_vs_mixed_sex_pool: brain

source_name: mouse66, brain


title: mouse61_vs_mixed_sex_pool: brain

source_name: mouse61, brain


title: mouse60_vs_mixed_sex_pool: brain

source_name: mouse60, brain


title: mouse73_vs_mixed_sex_pool: brain

source_name: mouse73, brain


title: mouse59_vs_mixed_sex_pool: brain

source_name: mouse59, brain


title: mouse62_vs_mixed_sex_pool: brain

source_name: mouse62, brain


title: mouse57_vs_mixed_sex_pool: brain

source_name: mouse57, brain


title: mouse56_vs_mixed_sex_pool: brain

source_name: mouse56, brain


title: mouse53_vs_mixed_sex_pool: brain

source_name: mouse53, brain


title: mouse48_vs_mixed_sex_pool: brain

source_name: mouse48, brain


title: mouse55_vs_mixed_sex_pool: brain

source_name: mouse55, brain


title: mouse54_vs_mixed_sex_pool: brain

source_name: mouse54, brain


title: mouse51_vs_mixed_sex_pool: brain

source_name: mouse51, brain


title: mouse58_vs_mixed_sex_pool: brain

source_name: mouse58, brain

source_name: reference pool (mixed sex, brain)


title: mouse50_vs_mixed_sex_pool: brain

source_name: mouse50, brain


title: mouse437_vs_male_pool: muscle

source_name: mouse437, muscle

value: muscle

source_name: reference pool (male, muscle)


title: mouse440_vs_male_pool: muscle

source_name: mouse440, muscle


title: mouse52_vs_mixed_sex_pool: brain

source_name: mouse52, brain


title: mouse49_vs_mixed_sex_pool: brain

source_name: mouse49, brain


title: mouse443_vs_male_pool: muscle

source_name: mouse443, muscle


title: mouse439_vs_male_pool: muscle

source_name: mouse439, muscle


title: mouse435_vs_male_pool: muscle

source_name: mouse435, muscle


title: mouse442_vs_male_pool: muscle

source_name: mouse442, muscle


title: mouse436_vs_male_pool: muscle

source_name: mouse436, muscle


title: mouse432_vs_male_pool: muscle

source_name: mouse432, muscle


title: mouse441_vs_male_pool: muscle

source_name: mouse441, muscle


title: mouse433_vs_male_pool: muscle

source_name: mouse433, muscle


title: mouse438_vs_male_pool: muscle

source_name: mouse438, muscle


title: mouse431_vs_male_pool: muscle

source_name: mouse431, muscle


title: mouse429_vs_male_pool: muscle

source_name: mouse429, muscle


title: mouse434_vs_male_pool: muscle

source_name: mouse434, muscle


title: mouse430_vs_male_pool: muscle

source_name: mouse430, muscle


title: mouse72_vs_mixed_sex_pool: brain

source_name: mouse72, brain

source_name: reference pool (mixed sex, brain)


title: mouse422_vs_male_pool: muscle

source_name: mouse422, muscle

source_name: reference pool (male, muscle)


title: mouse427_vs_male_pool: muscle

source_name: mouse427, muscle


title: mouse414_vs_male_pool: muscle

source_name: mouse414, muscle


title: mouse428_vs_male_pool: muscle

source_name: mouse428, muscle


title: mouse412_vs_male_pool: muscle

source_name: mouse412, muscle


title: mouse408_vs_male_pool: muscle

source_name: mouse408, muscle


title: mouse411_vs_male_pool: muscle

source_name: mouse411, muscle


title: mouse416_vs_male_pool: muscle

source_name: mouse416, muscle


title: mouse418_vs_male_pool: muscle

source_name: mouse418, muscle


title: mouse406_vs_male_pool: muscle

source_name: mouse406, muscle


title: mouse420_vs_male_pool: muscle

source_name: mouse420, muscle


title: mouse426_vs_male_pool: muscle

source_name: mouse426, muscle


title: mouse425_vs_male_pool: muscle

source_name: mouse425, muscle


title: mouse413_vs_male_pool: muscle

source_name: mouse413, muscle


title: mouse423_vs_male_pool: muscle

source_name: mouse423, muscle


title: mouse417_vs_male_pool: muscle

source_name: mouse417, muscle


title: mouse410_vs_male_pool: muscle

source_name: mouse410, muscle


title: mouse424_vs_male_pool: muscle

source_name: mouse424, muscle

source_name: reference pool (male, muscle)


title: mouse421_vs_male_pool: muscle

source_name: mouse421, muscle


title: mouse419_vs_male_pool: muscle

source_name: mouse419, muscle


title: mouse409_vs_male_pool: muscle

source_name: mouse409, muscle


title: mouse404_vs_male_pool: muscle

source_name: mouse404, muscle


title: mouse405_vs_male_pool: muscle

source_name: mouse405, muscle


title: mouse415_vs_male_pool: muscle

source_name: mouse415, muscle


title: mouse407_vs_male_pool: muscle

source_name: mouse407, muscle


title: mouse400_vs_male_pool: muscle

source_name: mouse400, muscle


title: mouse403_vs_male_pool: muscle

source_name: mouse403, muscle


title: mouse401_vs_male_pool: muscle

source_name: mouse401, muscle


title: mouse392_vs_male_pool: muscle

source_name: mouse392, muscle


title: mouse387_vs_male_pool: muscle

source_name: mouse387, muscle


title: mouse396_vs_male_pool: muscle

source_name: mouse396, muscle


title: mouse394_vs_male_pool: muscle

source_name: mouse394, muscle


title: mouse391_vs_male_pool: muscle

source_name: mouse391, muscle


title: mouse386_vs_male_pool: muscle

source_name: mouse386, muscle


title: mouse389_vs_male_pool: muscle

source_name: mouse389, muscle

source_name: reference pool (male, muscle)


title: mouse390_vs_male_pool: muscle

source_name: mouse390, muscle


title: mouse399_vs_male_pool: muscle

source_name: mouse399, muscle


title: mouse397_vs_male_pool: muscle

source_name: mouse397, muscle


title: mouse398_vs_male_pool: muscle

source_name: mouse398, muscle


title: mouse395_vs_male_pool: muscle

source_name: mouse395, muscle


title: mouse384_vs_male_pool: muscle

source_name: mouse384, muscle


title: mouse393_vs_male_pool: muscle

source_name: mouse393, muscle


title: mouse381_vs_male_pool: muscle

source_name: mouse381, muscle


title: mouse385_vs_male_pool: muscle

source_name: mouse385, muscle


title: mouse388_vs_male_pool: muscle

source_name: mouse388, muscle


title: mouse382_vs_male_pool: muscle

source_name: mouse382, muscle


title: mouse383_vs_male_pool: muscle

source_name: mouse383, muscle


title: mouse379_vs_male_pool: muscle

source_name: mouse379, muscle


title: mouse377_vs_male_pool: muscle

source_name: mouse377, muscle


title: mouse378_vs_male_pool: muscle

source_name: mouse378, muscle


title: mouse376_vs_male_pool: muscle

source_name: mouse376, muscle


title: mouse374_vs_male_pool: muscle

source_name: mouse374, muscle

source_name: reference pool (male, muscle)


title: mouse364_vs_male_pool: muscle

source_name: mouse364, muscle


title: mouse370_vs_male_pool: muscle

source_name: mouse370, muscle


title: mouse373_vs_male_pool: muscle

source_name: mouse373, muscle


title: mouse369_vs_male_pool: muscle

source_name: mouse369, muscle


title: mouse371_vs_male_pool: muscle

source_name: mouse371, muscle


title: mouse366_vs_male_pool: muscle

source_name: mouse366, muscle


title: mouse365_vs_male_pool: muscle

source_name: mouse365, muscle


title: mouse372_vs_male_pool: muscle

source_name: mouse372, muscle


title: mouse375_vs_male_pool: muscle

source_name: mouse375, muscle


title: mouse367_vs_male_pool: muscle

source_name: mouse367, muscle


title: mouse361_vs_male_pool: muscle

source_name: mouse361, muscle


title: mouse363_vs_male_pool: muscle

source_name: mouse363, muscle


title: mouse368_vs_male_pool: muscle

source_name: mouse368, muscle


title: mouse362_vs_male_pool: muscle

source_name: mouse362, muscle


title: mouse359_vs_male_pool: muscle

source_name: mouse359, muscle


title: mouse356_vs_male_pool: muscle

source_name: mouse356, muscle


title: mouse354_vs_male_pool: muscle

source_name: mouse354, muscle

source_name: reference pool (male, muscle)


title: mouse357_vs_male_pool: muscle

source_name: mouse357, muscle


title: mouse360_vs_male_pool: muscle

source_name: mouse360, muscle


title: mouse353_vs_male_pool: muscle

source_name: mouse353, muscle


title: mouse355_vs_male_pool: muscle

source_name: mouse355, muscle


title: mouse352_vs_male_pool: muscle

source_name: mouse352, muscle


title: mouse358_vs_male_pool: muscle

source_name: mouse358, muscle


title: mouse402_vs_male_pool: muscle

source_name: mouse402, muscle


title: mouse380_vs_male_pool: muscle

source_name: mouse380, muscle


title: mouse342_vs_male_pool: muscle

source_name: mouse342, muscle


title: mouse349_vs_male_pool: muscle

source_name: mouse349, muscle


title: mouse350_vs_male_pool: muscle

source_name: mouse350, muscle


title: mouse343_vs_male_pool: muscle

source_name: mouse343, muscle


title: mouse344_vs_male_pool: muscle

source_name: mouse344, muscle


title: mouse351_vs_male_pool: muscle

source_name: mouse351, muscle


title: mouse339_vs_male_pool: muscle

source_name: mouse339, muscle


title: mouse340_vs_male_pool: muscle

source_name: mouse340, muscle


title: mouse341_vs_male_pool: muscle

source_name: mouse341, muscle

source_name: reference pool (male, muscle)


title: mouse345_vs_male_pool: muscle

source_name: mouse345, muscle


title: mouse337_vs_male_pool: muscle

source_name: mouse337, muscle


title: mouse346_vs_male_pool: muscle

source_name: mouse346, muscle


title: mouse333_vs_male_pool: muscle

source_name: mouse333, muscle


title: mouse336_vs_male_pool: muscle

source_name: mouse336, muscle


title: mouse335_vs_male_pool: muscle

source_name: mouse335, muscle


title: mouse347_vs_male_pool: muscle

source_name: mouse347, muscle


title: mouse334_vs_male_pool: muscle

source_name: mouse334, muscle


title: mouse332_vs_male_pool: muscle

source_name: mouse332, muscle


title: mouse329_vs_male_pool: muscle

source_name: mouse329, muscle


title: mouse330_vs_male_pool: muscle

source_name: mouse330, muscle


title: mouse331_vs_male_pool: muscle

source_name: mouse331, muscle


title: mouse348_vs_male_pool: muscle

source_name: mouse348, muscle


title: mouse328_vs_male_pool: muscle

source_name: mouse328, muscle


title: mouse325_vs_male_pool: muscle

source_name: mouse325, muscle


title: mouse326_vs_male_pool: muscle

source_name: mouse326, muscle


title: mouse327_vs_male_pool: muscle

source_name: mouse327, muscle

source_name: reference pool (male, muscle)


title: mouse323_vs_male_pool: muscle

source_name: mouse323, muscle


title: mouse322_vs_male_pool: muscle

source_name: mouse322, muscle


title: mouse442_vs_male_pool: brain

source_name: mouse442, brain

source_name: reference pool (male, brain)


title: mouse441_vs_male_pool: brain

source_name: mouse441, brain


title: mouse440_vs_male_pool: brain

source_name: mouse440, brain


title: mouse436_vs_male_pool: brain

source_name: mouse436, brain


title: mouse437_vs_male_pool: brain

source_name: mouse437, brain


title: mouse438_vs_male_pool: brain

source_name: mouse438, brain


title: mouse443_vs_male_pool: brain

source_name: mouse443, brain


title: mouse433_vs_male_pool: brain

source_name: mouse433, brain


title: mouse435_vs_male_pool: brain

source_name: mouse435, brain


title: mouse439_vs_male_pool: brain

source_name: mouse439, brain


title: mouse430_vs_male_pool: brain

source_name: mouse430, brain


title: mouse434_vs_male_pool: brain

source_name: mouse434, brain


title: mouse431_vs_male_pool: brain

source_name: mouse431, brain


title: mouse432_vs_male_pool: brain

source_name: mouse432, brain


title: mouse338_vs_male_pool: muscle

source_name: mouse338, muscle

source_name: reference pool (male, muscle)


title: mouse428_vs_male_pool: brain

source_name: mouse428, brain


title: mouse427_vs_male_pool: brain

source_name: mouse427, brain

source_name: reference pool (male, brain)


title: mouse424_vs_male_pool: brain

source_name: mouse424, brain


title: mouse429_vs_male_pool: brain

source_name: mouse429, brain


title: mouse426_vs_male_pool: brain

source_name: mouse426, brain


title: mouse422_vs_male_pool: brain

source_name: mouse422, brain


title: mouse423_vs_male_pool: brain

source_name: mouse423, brain


title: mouse421_vs_male_pool: brain

source_name: mouse421, brain


title: mouse414_vs_male_pool: brain

source_name: mouse414, brain


title: mouse420_vs_male_pool: brain

source_name: mouse420, brain


title: mouse419_vs_male_pool: brain

source_name: mouse419, brain


title: mouse417_vs_male_pool: brain

source_name: mouse417, brain


title: mouse415_vs_male_pool: brain

source_name: mouse415, brain


title: mouse416_vs_male_pool: brain

source_name: mouse416, brain


title: mouse413_vs_male_pool: brain

source_name: mouse413, brain


title: mouse412_vs_male_pool: brain

source_name: mouse412, brain


title: mouse405_vs_male_pool: brain

source_name: mouse405, brain


title: mouse409_vs_male_pool: brain

source_name: mouse409, brain


title: mouse410_vs_male_pool: brain

source_name: mouse410, brain

source_name: reference pool (male, brain)


title: mouse407_vs_male_pool: brain

source_name: mouse407, brain


title: mouse404_vs_male_pool: brain

source_name: mouse404, brain


title: mouse408_vs_male_pool: brain

source_name: mouse408, brain


title: mouse403_vs_male_pool: brain

source_name: mouse403, brain


title: mouse425_vs_male_pool: brain

source_name: mouse425, brain


title: mouse411_vs_male_pool: brain

source_name: mouse411, brain


title: mouse402_vs_male_pool: brain

source_name: mouse402, brain


title: mouse406_vs_male_pool: brain

source_name: mouse406, brain


title: mouse400_vs_male_pool: brain

source_name: mouse400, brain


title: mouse399_vs_male_pool: brain

source_name: mouse399, brain


title: mouse398_vs_male_pool: brain

source_name: mouse398, brain


title: mouse401_vs_male_pool: brain

source_name: mouse401, brain


title: mouse397_vs_male_pool: brain

source_name: mouse397, brain


title: mouse394_vs_male_pool: brain

source_name: mouse394, brain


title: mouse392_vs_male_pool: brain

source_name: mouse392, brain


title: mouse393_vs_male_pool: brain

source_name: mouse393, brain


title: mouse396_vs_male_pool: brain

source_name: mouse396, brain

source_name: reference pool (male, brain)


title: mouse390_vs_male_pool: brain

source_name: mouse390, brain


title: mouse391_vs_male_pool: brain

source_name: mouse391, brain


title: mouse387_vs_male_pool: brain

source_name: mouse387, brain


title: mouse385_vs_male_pool: brain

source_name: mouse385, brain


title: mouse389_vs_male_pool: brain

source_name: mouse389, brain


title: mouse380_vs_male_pool: brain

source_name: mouse380, brain


title: mouse388_vs_male_pool: brain

source_name: mouse388, brain


title: mouse384_vs_male_pool: brain

source_name: mouse384, brain


title: mouse382_vs_male_pool: brain

source_name: mouse382, brain


title: mouse383_vs_male_pool: brain

source_name: mouse383, brain


title: mouse386_vs_male_pool: brain

source_name: mouse386, brain


title: mouse379_vs_male_pool: brain

source_name: mouse379, brain


title: mouse418_vs_male_pool: brain

source_name: mouse418, brain


title: mouse378_vs_male_pool: brain

source_name: mouse378, brain


title: mouse375_vs_male_pool: brain

source_name: mouse375, brain


title: mouse381_vs_male_pool: brain

source_name: mouse381, brain


title: mouse377_vs_male_pool: brain

source_name: mouse377, brain

source_name: reference pool (male, brain)


title: mouse376_vs_male_pool: brain

source_name: mouse376, brain


title: mouse395_vs_male_pool: brain

source_name: mouse395, brain


title: mouse374_vs_male_pool: brain

source_name: mouse374, brain


title: mouse373_vs_male_pool: brain

source_name: mouse373, brain


title: mouse372_vs_male_pool: brain

source_name: mouse372, brain


title: mouse371_vs_male_pool: brain

source_name: mouse371, brain


title: mouse365_vs_male_pool: brain

source_name: mouse365, brain


title: mouse361_vs_male_pool: brain

source_name: mouse361, brain


title: mouse362_vs_male_pool: brain

source_name: mouse362, brain


title: mouse363_vs_male_pool: brain

source_name: mouse363, brain


title: mouse360_vs_male_pool: brain

source_name: mouse360, brain


title: mouse356_vs_male_pool: brain

source_name: mouse356, brain


title: mouse366_vs_male_pool: brain

source_name: mouse366, brain


title: mouse368_vs_male_pool: brain

source_name: mouse368, brain


title: mouse357_vs_male_pool: brain

source_name: mouse357, brain


title: mouse369_vs_male_pool: brain

source_name: mouse369, brain


title: mouse364_vs_male_pool: brain

source_name: mouse364, brain

source_name: reference pool (male, brain)


title: mouse367_vs_male_pool: brain

source_name: mouse367, brain


title: mouse358_vs_male_pool: brain

source_name: mouse358, brain


title: mouse352_vs_male_pool: brain

source_name: mouse352, brain


title: mouse359_vs_male_pool: brain

source_name: mouse359, brain


title: mouse370_vs_male_pool: brain

source_name: mouse370, brain


title: mouse353_vs_male_pool: brain

source_name: mouse353, brain


title: mouse351_vs_male_pool: brain

source_name: mouse351, brain


title: mouse354_vs_male_pool: brain

source_name: mouse354, brain


title: mouse355_vs_male_pool: brain

source_name: mouse355, brain


title: mouse349_vs_male_pool: brain

source_name: mouse349, brain


title: mouse348_vs_male_pool: brain

source_name: mouse348, brain


title: mouse350_vs_male_pool: brain

source_name: mouse350, brain


title: mouse343_vs_male_pool: brain

source_name: mouse343, brain


title: mouse345_vs_male_pool: brain

source_name: mouse345, brain


title: mouse338_vs_male_pool: brain

source_name: mouse338, brain


title: mouse340_vs_male_pool: brain

source_name: mouse340, brain


title: mouse347_vs_male_pool: brain

source_name: mouse347, brain

source_name: reference pool (male, brain)


title: mouse344_vs_male_pool: brain

source_name: mouse344, brain


title: mouse341_vs_male_pool: brain

source_name: mouse341, brain


title: mouse337_vs_male_pool: brain

source_name: mouse337, brain


title: mouse334_vs_male_pool: brain

source_name: mouse334, brain


title: mouse331_vs_male_pool: brain

source_name: mouse331, brain


title: mouse346_vs_male_pool: brain

source_name: mouse346, brain


title: mouse328_vs_male_pool: brain

source_name: mouse328, brain


title: mouse333_vs_male_pool: brain

source_name: mouse333, brain


title: mouse332_vs_male_pool: brain

source_name: mouse332, brain


title: mouse329_vs_male_pool: brain

source_name: mouse329, brain


title: mouse336_vs_male_pool: brain

source_name: mouse336, brain


title: mouse327_vs_male_pool: brain

source_name: mouse327, brain


title: mouse335_vs_male_pool: brain

source_name: mouse335, brain


title: mouse339_vs_male_pool: brain

source_name: mouse339, brain


title: mouse342_vs_male_pool: brain

source_name: mouse342, brain


title: mouse326_vs_male_pool: brain

source_name: mouse326, brain


title: mouse330_vs_male_pool: brain

source_name: mouse330, brain

source_name: reference pool (male, brain)


title: mouse323_vs_male_pool: brain

source_name: mouse323, brain


title: mouse325_vs_male_pool: brain

source_name: mouse325, brain


title: mouse324_vs_male_pool: brain

source_name: mouse324, brain


title: mouse322_vs_male_pool: brain

source_name: mouse322, brain


title: mouse439_vs_male_pool: liver

source_name: mouse439, liver

value: liver

source_name: reference pool (male, liver)


title: mouse441_vs_male_pool: liver

source_name: mouse441, liver


title: mouse442_vs_male_pool: liver

source_name: mouse442, liver


title: mouse434_vs_male_pool: liver

source_name: mouse434, liver


title: mouse436_vs_male_pool: liver

source_name: mouse436, liver


title: mouse438_vs_male_pool: liver

source_name: mouse438, liver


title: mouse429_vs_male_pool: liver

source_name: mouse429, liver


title: mouse431_vs_male_pool: liver

source_name: mouse431, liver


title: mouse433_vs_male_pool: liver

source_name: mouse433, liver


title: mouse437_vs_male_pool: liver

source_name: mouse437, liver


title: mouse435_vs_male_pool: liver

source_name: mouse435, liver


title: mouse424_vs_male_pool: liver

source_name: mouse424, liver


title: mouse430_vs_male_pool: liver

source_name: mouse430, liver


title: mouse425_vs_male_pool: liver

source_name: mouse425, liver


title: mouse427_vs_male_pool: liver

source_name: mouse427, liver


title: mouse428_vs_male_pool: liver

source_name: mouse428, liver


title: mouse432_vs_male_pool: liver

source_name: mouse432, liver


title: mouse426_vs_male_pool: liver

source_name: mouse426, liver

source_name: reference pool (male, liver)


title: mouse423_vs_male_pool: liver

source_name: mouse423, liver


title: mouse443_vs_male_pool: liver

source_name: mouse443, liver


title: mouse440_vs_male_pool: liver

source_name: mouse440, liver


title: mouse417_vs_male_pool: liver

source_name: mouse417, liver


title: mouse418_vs_male_pool: liver

source_name: mouse418, liver


title: mouse419_vs_male_pool: liver

source_name: mouse419, liver


title: mouse420_vs_male_pool: liver

source_name: mouse420, liver


title: mouse422_vs_male_pool: liver

source_name: mouse422, liver


title: mouse415_vs_male_pool: liver

source_name: mouse415, liver


title: mouse421_vs_male_pool: liver

source_name: mouse421, liver


title: mouse414_vs_male_pool: liver

source_name: mouse414, liver


title: mouse413_vs_male_pool: liver

source_name: mouse413, liver


title: mouse416_vs_male_pool: liver

source_name: mouse416, liver


title: mouse404_vs_male_pool: liver

source_name: mouse404, liver


title: mouse410_vs_male_pool: liver

source_name: mouse410, liver


title: mouse408_vs_male_pool: liver

source_name: mouse408, liver


title: mouse401_vs_male_pool: liver

source_name: mouse401, liver

source_name: reference pool (male, liver)


title: mouse402_vs_male_pool: liver

source_name: mouse402, liver


title: mouse407_vs_male_pool: liver

source_name: mouse407, liver


title: mouse411_vs_male_pool: liver

source_name: mouse411, liver


title: mouse398_vs_male_pool: liver

source_name: mouse398, liver


title: mouse403_vs_male_pool: liver

source_name: mouse403, liver


title: mouse409_vs_male_pool: liver

source_name: mouse409, liver


title: mouse405_vs_male_pool: liver

source_name: mouse405, liver


title: mouse400_vs_male_pool: liver

source_name: mouse400, liver


title: mouse412_vs_male_pool: liver

source_name: mouse412, liver


title: mouse406_vs_male_pool: liver

source_name: mouse406, liver


title: mouse399_vs_male_pool: liver

source_name: mouse399, liver


title: mouse390_vs_male_pool: liver

source_name: mouse390, liver


title: mouse393_vs_male_pool: liver

source_name: mouse393, liver


title: mouse394_vs_male_pool: liver

source_name: mouse394, liver


title: mouse395_vs_male_pool: liver

source_name: mouse395, liver


title: mouse391_vs_male_pool: liver

source_name: mouse391, liver


title: mouse397_vs_male_pool: liver

source_name: mouse397, liver

source_name: reference pool (male, liver)


title: mouse396_vs_male_pool: liver

source_name: mouse396, liver


title: mouse388_vs_male_pool: liver

source_name: mouse388, liver


title: mouse389_vs_male_pool: liver

source_name: mouse389, liver


title: mouse387_vs_male_pool: liver

source_name: mouse387, liver


title: mouse392_vs_male_pool: liver

source_name: mouse392, liver


title: mouse382_vs_male_pool: liver

source_name: mouse382, liver


title: mouse380_vs_male_pool: liver

source_name: mouse380, liver


title: mouse378_vs_male_pool: liver

source_name: mouse378, liver


title: mouse379_vs_male_pool: liver

source_name: mouse379, liver


title: mouse377_vs_male_pool: liver

source_name: mouse377, liver


title: mouse381_vs_male_pool: liver

source_name: mouse381, liver


title: mouse386_vs_male_pool: liver

source_name: mouse386, liver


title: mouse384_vs_male_pool: liver

source_name: mouse384, liver


title: mouse376_vs_male_pool: liver

source_name: mouse376, liver


title: mouse375_vs_male_pool: liver

source_name: mouse375, liver


title: mouse374_vs_male_pool: liver

source_name: mouse374, liver


title: mouse372_vs_male_pool: liver

source_name: mouse372, liver

source_name: reference pool (male, liver)


title: mouse373_vs_male_pool: liver

source_name: mouse373, liver


title: mouse371_vs_male_pool: liver

source_name: mouse371, liver


title: mouse369_vs_male_pool: liver

source_name: mouse369, liver


title: mouse367_vs_male_pool: liver

source_name: mouse367, liver


title: mouse368_vs_male_pool: liver

source_name: mouse368, liver


title: mouse364_vs_male_pool: liver

source_name: mouse364, liver


title: mouse365_vs_male_pool: liver

source_name: mouse365, liver


title: mouse370_vs_male_pool: liver

source_name: mouse370, liver


title: mouse366_vs_male_pool: liver

source_name: mouse366, liver


title: mouse360_vs_male_pool: liver

source_name: mouse360, liver


title: mouse385_vs_male_pool: liver

source_name: mouse385, liver


title: mouse383_vs_male_pool: liver

source_name: mouse383, liver


title: mouse363_vs_male_pool: liver

source_name: mouse363, liver


title: mouse361_vs_male_pool: liver

source_name: mouse361, liver


title: mouse356_vs_male_pool: liver

source_name: mouse356, liver


title: mouse355_vs_male_pool: liver

source_name: mouse355, liver


title: mouse359_vs_male_pool: liver

source_name: mouse359, liver

source_name: reference pool (male, liver)


title: mouse350_vs_male_pool: liver

source_name: mouse350, liver


title: mouse357_vs_male_pool: liver

source_name: mouse357, liver


title: mouse351_vs_male_pool: liver

source_name: mouse351, liver


title: mouse354_vs_male_pool: liver

source_name: mouse354, liver


title: mouse348_vs_male_pool: liver

source_name: mouse348, liver


title: mouse353_vs_male_pool: liver

source_name: mouse353, liver


title: mouse358_vs_male_pool: liver

source_name: mouse358, liver


title: mouse349_vs_male_pool: liver

source_name: mouse349, liver


title: mouse347_vs_male_pool: liver

source_name: mouse347, liver


title: mouse352_vs_male_pool: liver

source_name: mouse352, liver


title: mouse362_vs_male_pool: liver

source_name: mouse362, liver


title: mouse343_vs_male_pool: liver

source_name: mouse343, liver


title: mouse342_vs_male_pool: liver

source_name: mouse342, liver


title: mouse345_vs_male_pool: liver

source_name: mouse345, liver


title: mouse341_vs_male_pool: liver

source_name: mouse341, liver


title: mouse340_vs_male_pool: liver

source_name: mouse340, liver


title: mouse344_vs_male_pool: liver

source_name: mouse344, liver

source_name: reference pool (male, liver)


title: mouse338_vs_male_pool: liver

source_name: mouse338, liver


title: mouse339_vs_male_pool: liver

source_name: mouse339, liver


title: mouse346_vs_male_pool: liver

source_name: mouse346, liver


title: mouse333_vs_male_pool: liver

source_name: mouse333, liver


title: mouse336_vs_male_pool: liver

source_name: mouse336, liver


title: mouse334_vs_male_pool: liver

source_name: mouse334, liver


title: mouse335_vs_male_pool: liver

source_name: mouse335, liver


title: mouse328_vs_male_pool: liver

source_name: mouse328, liver


title: mouse337_vs_male_pool: liver

source_name: mouse337, liver


title: mouse330_vs_male_pool: liver

source_name: mouse330, liver


title: mouse329_vs_male_pool: liver

source_name: mouse329, liver


title: mouse331_vs_male_pool: liver

source_name: mouse331, liver


title: mouse324_vs_male_pool: liver

source_name: mouse324, liver


title: mouse326_vs_male_pool: liver

source_name: mouse326, liver


title: mouse332_vs_male_pool: liver

source_name: mouse332, liver


title: mouse325_vs_male_pool: liver

source_name: mouse325, liver


title: mouse327_vs_male_pool: liver

source_name: mouse327, liver

source_name: reference pool (male, liver)


title: mouse322_vs_male_pool: liver

source_name: mouse322, liver


title: mouse323_vs_male_pool: liver

source_name: mouse323, liver


title: mouse321_vs_female_pool: muscle

source_name: mouse321, muscle

source_name: reference pool (female, muscle)


title: mouse320_vs_female_pool: muscle

source_name: mouse320, muscle


title: mouse319_vs_female_pool: muscle

source_name: mouse319, muscle


title: mouse317_vs_female_pool: muscle

source_name: mouse317, muscle


title: mouse312_vs_female_pool: muscle

source_name: mouse312, muscle


title: mouse313_vs_female_pool: muscle

source_name: mouse313, muscle


title: mouse314_vs_female_pool: muscle

source_name: mouse314, muscle


title: mouse308_vs_female_pool: muscle

source_name: mouse308, muscle


title: mouse318_vs_female_pool: muscle

source_name: mouse318, muscle


title: mouse316_vs_female_pool: muscle

source_name: mouse316, muscle


title: mouse315_vs_female_pool: muscle

source_name: mouse315, muscle


title: mouse304_vs_female_pool: muscle

source_name: mouse304, muscle


title: mouse307_vs_female_pool: muscle

source_name: mouse307, muscle


title: mouse310_vs_female_pool: muscle

source_name: mouse310, muscle


title: mouse303_vs_female_pool: muscle

source_name: mouse303, muscle


title: mouse297_vs_female_pool: muscle

source_name: mouse297, muscle


title: mouse299_vs_female_pool: muscle

source_name: mouse299, muscle


title: mouse311_vs_female_pool: muscle

source_name: mouse311, muscle

source_name: reference pool (female, muscle)


title: mouse305_vs_female_pool: muscle

source_name: mouse305, muscle


title: mouse298_vs_female_pool: muscle

source_name: mouse298, muscle


title: mouse306_vs_female_pool: muscle

source_name: mouse306, muscle


title: mouse301_vs_female_pool: muscle

source_name: mouse301, muscle


title: mouse302_vs_female_pool: muscle

source_name: mouse302, muscle


title: mouse294_vs_female_pool: muscle

source_name: mouse294, muscle


title: mouse295_vs_female_pool: muscle

source_name: mouse295, muscle


title: mouse293_vs_female_pool: muscle

source_name: mouse293, muscle


title: mouse309_vs_female_pool: muscle

source_name: mouse309, muscle


title: mouse300_vs_female_pool: muscle

source_name: mouse300, muscle


title: mouse292_vs_female_pool: muscle

source_name: mouse292, muscle


title: mouse291_vs_female_pool: muscle

source_name: mouse291, muscle


title: mouse290_vs_female_pool: muscle

source_name: mouse290, muscle


title: mouse284_vs_female_pool: muscle

source_name: mouse284, muscle


title: mouse283_vs_female_pool: muscle

source_name: mouse283, muscle


title: mouse296_vs_female_pool: muscle

source_name: mouse296, muscle


title: mouse286_vs_female_pool: muscle

source_name: mouse286, muscle

source_name: reference pool (female, muscle)


title: mouse289_vs_female_pool: muscle

source_name: mouse289, muscle


title: mouse288_vs_female_pool: muscle

source_name: mouse288, muscle


title: mouse282_vs_female_pool: muscle

source_name: mouse282, muscle


title: mouse275_vs_female_pool: muscle

source_name: mouse275, muscle


title: mouse281_vs_female_pool: muscle

source_name: mouse281, muscle


title: mouse287_vs_female_pool: muscle

source_name: mouse287, muscle


title: mouse285_vs_female_pool: muscle

source_name: mouse285, muscle


title: mouse273_vs_female_pool: muscle

source_name: mouse273, muscle


title: mouse278_vs_female_pool: muscle

source_name: mouse278, muscle


title: mouse268_vs_female_pool: muscle

source_name: mouse268, muscle


title: mouse271_vs_female_pool: muscle

source_name: mouse271, muscle


title: mouse280_vs_female_pool: muscle

source_name: mouse280, muscle


title: mouse269_vs_female_pool: muscle

source_name: mouse269, muscle


title: mouse279_vs_female_pool: muscle

source_name: mouse279, muscle


title: mouse276_vs_female_pool: muscle

source_name: mouse276, muscle


title: mouse277_vs_female_pool: muscle

source_name: mouse277, muscle


title: mouse265_vs_female_pool: muscle

source_name: mouse265, muscle

source_name: reference pool (female, muscle)


title: mouse263_vs_female_pool: muscle

source_name: mouse263, muscle


title: mouse274_vs_female_pool: muscle

source_name: mouse274, muscle


title: mouse272_vs_female_pool: muscle

source_name: mouse272, muscle


title: mouse262_vs_female_pool: muscle

source_name: mouse262, muscle


title: mouse264_vs_female_pool: muscle

source_name: mouse264, muscle


title: mouse253_vs_female_pool: muscle

source_name: mouse253, muscle


title: mouse255_vs_female_pool: muscle

source_name: mouse255, muscle


title: mouse251_vs_female_pool: muscle

source_name: mouse251, muscle


title: mouse250_vs_female_pool: muscle

source_name: mouse250, muscle


title: mouse249_vs_female_pool: muscle

source_name: mouse249, muscle


title: mouse270_vs_female_pool: muscle

source_name: mouse270, muscle


title: mouse242_vs_female_pool: muscle

source_name: mouse242, muscle


title: mouse247_vs_female_pool: muscle

source_name: mouse247, muscle


title: mouse261_vs_female_pool: muscle

source_name: mouse261, muscle


title: mouse267_vs_female_pool: muscle

source_name: mouse267, muscle


title: mouse260_vs_female_pool: muscle

source_name: mouse260, muscle


title: mouse259_vs_female_pool: muscle

source_name: mouse259, muscle

source_name: reference pool (female, muscle)


title: mouse266_vs_female_pool: muscle

source_name: mouse266, muscle


title: mouse239_vs_female_pool: muscle

source_name: mouse239, muscle


title: mouse240_vs_female_pool: muscle

source_name: mouse240, muscle


title: mouse256_vs_female_pool: muscle

source_name: mouse256, muscle


title: mouse258_vs_female_pool: muscle

source_name: mouse258, muscle


title: mouse254_vs_female_pool: muscle

source_name: mouse254, muscle


title: mouse257_vs_female_pool: muscle

source_name: mouse257, muscle


title: mouse248_vs_female_pool: muscle

source_name: mouse248, muscle


title: mouse243_vs_female_pool: muscle

source_name: mouse243, muscle


title: mouse246_vs_female_pool: muscle

source_name: mouse246, muscle


title: mouse238_vs_female_pool: muscle

source_name: mouse238, muscle


title: mouse244_vs_female_pool: muscle

source_name: mouse244, muscle


title: mouse232_vs_female_pool: muscle

source_name: mouse232, muscle


title: mouse245_vs_female_pool: muscle

source_name: mouse245, muscle


title: mouse241_vs_female_pool: muscle

source_name: mouse241, muscle


title: mouse252_vs_female_pool: muscle

source_name: mouse252, muscle


title: mouse236_vs_female_pool: muscle

source_name: mouse236, muscle

source_name: reference pool (female, muscle)


title: mouse233_vs_female_pool: muscle

source_name: mouse233, muscle


title: mouse237_vs_female_pool: muscle

source_name: mouse237, muscle


title: mouse234_vs_female_pool: muscle

source_name: mouse234, muscle


title: mouse228_vs_female_pool: muscle

source_name: mouse228, muscle


title: mouse231_vs_female_pool: muscle

source_name: mouse231, muscle


title: mouse229_vs_female_pool: muscle

source_name: mouse229, muscle


title: mouse225_vs_female_pool: muscle

source_name: mouse225, muscle


title: mouse224_vs_female_pool: muscle

source_name: mouse224, muscle


title: mouse223_vs_female_pool: muscle

source_name: mouse223, muscle


title: mouse221_vs_female_pool: muscle

source_name: mouse221, muscle


title: mouse230_vs_female_pool: muscle

source_name: mouse230, muscle


title: mouse226_vs_female_pool: muscle

source_name: mouse226, muscle


title: mouse227_vs_female_pool: muscle

source_name: mouse227, muscle


title: mouse220_vs_female_pool: muscle

source_name: mouse220, muscle


title: mouse222_vs_female_pool: muscle

source_name: mouse222, muscle


title: mouse217_vs_female_pool: muscle

source_name: mouse217, muscle


title: mouse218_vs_female_pool: muscle

source_name: mouse218, muscle

source_name: reference pool (female, muscle)


title: mouse214_vs_female_pool: muscle

source_name: mouse214, muscle


title: mouse219_vs_female_pool: muscle

source_name: mouse219, muscle


title: mouse212_vs_female_pool: muscle

source_name: mouse212, muscle


title: mouse210_vs_female_pool: muscle

source_name: mouse210, muscle


title: mouse211_vs_female_pool: muscle

source_name: mouse211, muscle


title: mouse213_vs_female_pool: muscle

source_name: mouse213, muscle


title: mouse207_vs_female_pool: muscle

source_name: mouse207, muscle


title: mouse216_vs_female_pool: muscle

source_name: mouse216, muscle


title: mouse215_vs_female_pool: muscle

source_name: mouse215, muscle


title: mouse203_vs_female_pool: muscle

source_name: mouse203, muscle


title: mouse209_vs_female_pool: muscle

source_name: mouse209, muscle


title: mouse206_vs_female_pool: muscle

source_name: mouse206, muscle


title: mouse205_vs_female_pool: muscle

source_name: mouse205, muscle


title: mouse202_vs_female_pool: muscle

source_name: mouse202, muscle


title: mouse204_vs_female_pool: muscle

source_name: mouse204, muscle


title: mouse208_vs_female_pool: muscle

source_name: mouse208, muscle


title: mouse201_vs_female_pool: muscle

source_name: mouse201, muscle

source_name: reference pool (female, muscle)


title: mouse200_vs_female_pool: muscle

source_name: mouse200, muscle


title: mouse199_vs_female_pool: muscle

source_name: mouse199, muscle


title: mouse198_vs_female_pool: muscle

source_name: mouse198, muscle


title: mouse196_vs_female_pool: muscle

source_name: mouse196, muscle


title: mouse194_vs_female_pool: muscle

source_name: mouse194, muscle


title: mouse195_vs_female_pool: muscle

source_name: mouse195, muscle


title: mouse197_vs_female_pool: muscle

source_name: mouse197, muscle


title: mouse186_vs_female_pool: muscle

source_name: mouse186, muscle


title: mouse187_vs_female_pool: muscle

source_name: mouse187, muscle


title: mouse192_vs_female_pool: muscle

source_name: mouse192, muscle


title: mouse180_vs_female_pool: muscle

source_name: mouse180, muscle


title: mouse188_vs_female_pool: muscle

source_name: mouse188, muscle


title: mouse182_vs_female_pool: muscle

source_name: mouse182, muscle


title: mouse185_vs_female_pool: muscle

source_name: mouse185, muscle


title: mouse191_vs_female_pool: muscle

source_name: mouse191, muscle


title: mouse176_vs_female_pool: muscle

source_name: mouse176, muscle


title: mouse184_vs_female_pool: muscle

source_name: mouse184, muscle

source_name: reference pool (female, muscle)


title: mouse177_vs_female_pool: muscle

source_name: mouse177, muscle


title: mouse193_vs_female_pool: muscle

source_name: mouse193, muscle


title: mouse178_vs_female_pool: muscle

source_name: mouse178, muscle


title: mouse179_vs_female_pool: muscle

source_name: mouse179, muscle


title: mouse181_vs_female_pool: muscle

source_name: mouse181, muscle


title: mouse190_vs_female_pool: muscle

source_name: mouse190, muscle


title: mouse183_vs_female_pool: muscle

source_name: mouse183, muscle


title: mouse189_vs_female_pool: muscle

source_name: mouse189, muscle


title: mouse175_vs_female_pool: muscle

source_name: mouse175, muscle


title: mouse173_vs_female_pool: muscle

source_name: mouse173, muscle


title: mouse171_vs_female_pool: muscle

source_name: mouse171, muscle


title: mouse174_vs_female_pool: muscle

source_name: mouse174, muscle


title: mouse170_vs_female_pool: muscle

source_name: mouse170, muscle


title: mouse172_vs_female_pool: muscle

source_name: mouse172, muscle


title: mouse167_vs_female_pool: muscle

source_name: mouse167, muscle


title: mouse168_vs_female_pool: muscle

source_name: mouse168, muscle


title: mouse169_vs_female_pool: muscle

source_name: mouse169, muscle

source_name: reference pool (female, muscle)


title: mouse162_vs_female_pool: muscle

source_name: mouse162, muscle


title: mouse157_vs_female_pool: muscle

source_name: mouse157, muscle


title: mouse159_vs_female_pool: muscle

source_name: mouse159, muscle


title: mouse165_vs_female_pool: muscle

source_name: mouse165, muscle


title: mouse166_vs_female_pool: muscle

source_name: mouse166, muscle


title: mouse154_vs_female_pool: muscle

source_name: mouse154, muscle


title: mouse156_vs_female_pool: muscle

source_name: mouse156, muscle


title: mouse160_vs_female_pool: muscle

source_name: mouse160, muscle


title: mouse163_vs_female_pool: muscle

source_name: mouse163, muscle


title: mouse153_vs_female_pool: muscle

source_name: mouse153, muscle


title: mouse158_vs_female_pool: muscle

source_name: mouse158, muscle


title: mouse161_vs_female_pool: muscle

source_name: mouse161, muscle


title: mouse151_vs_female_pool: muscle

source_name: mouse151, muscle


title: mouse155_vs_female_pool: muscle

source_name: mouse155, muscle


title: mouse152_vs_female_pool: muscle

source_name: mouse152, muscle


title: mouse164_vs_female_pool: muscle

source_name: mouse164, muscle


title: mouse149_vs_female_pool: muscle

source_name: mouse149, muscle

source_name: reference pool (female, muscle)


title: mouse146_vs_female_pool: muscle

source_name: mouse146, muscle


title: mouse150_vs_female_pool: muscle

source_name: mouse150, muscle


title: mouse148_vs_female_pool: muscle

source_name: mouse148, muscle


title: mouse147_vs_female_pool: muscle

source_name: mouse147, muscle


title: mouse145_vs_female_pool: muscle

source_name: mouse145, muscle


title: mouse142_vs_female_pool: muscle

source_name: mouse142, muscle


title: mouse141_vs_female_pool: muscle

source_name: mouse141, muscle


title: mouse140_vs_female_pool: muscle

source_name: mouse140, muscle


title: mouse138_vs_female_pool: muscle

source_name: mouse138, muscle


title: mouse128_vs_female_pool: muscle

source_name: mouse128, muscle


title: mouse129_vs_female_pool: muscle

source_name: mouse129, muscle


title: mouse135_vs_female_pool: muscle

source_name: mouse135, muscle


title: mouse144_vs_female_pool: muscle

source_name: mouse144, muscle


title: mouse132_vs_female_pool: muscle

source_name: mouse132, muscle


title: mouse133_vs_female_pool: muscle

source_name: mouse133, muscle


title: mouse143_vs_female_pool: muscle

source_name: mouse143, muscle


title: mouse139_vs_female_pool: muscle

source_name: mouse139, muscle

source_name: reference pool (female, muscle)


title: mouse127_vs_female_pool: muscle

source_name: mouse127, muscle


title: mouse137_vs_female_pool: muscle

source_name: mouse137, muscle


title: mouse134_vs_female_pool: muscle

source_name: mouse134, muscle


title: mouse130_vs_female_pool: muscle

source_name: mouse130, muscle


title: mouse131_vs_female_pool: muscle

source_name: mouse131, muscle


title: mouse126_vs_female_pool: muscle

source_name: mouse126, muscle


title: mouse136_vs_female_pool: muscle

source_name: mouse136, muscle


title: mouse123_vs_female_pool: muscle

source_name: mouse123, muscle


title: mouse122_vs_female_pool: muscle

source_name: mouse122, muscle


title: mouse124_vs_female_pool: muscle

source_name: mouse124, muscle


title: mouse125_vs_female_pool: muscle

source_name: mouse125, muscle


title: mouse121_vs_female_pool: muscle

source_name: mouse121, muscle


title: mouse120_vs_female_pool: muscle

source_name: mouse120, muscle


title: mouse119_vs_female_pool: muscle

source_name: mouse119, muscle


title: mouse117_vs_female_pool: muscle

source_name: mouse117, muscle


title: mouse315_vs_female_pool: brain

source_name: mouse315, brain

source_name: reference pool (female, brain)


title: mouse316_vs_female_pool: brain

source_name: mouse316, brain


title: mouse317_vs_female_pool: brain

source_name: mouse317, brain


title: mouse116_vs_female_pool: muscle

source_name: mouse116, muscle

source_name: reference pool (female, muscle)


title: mouse311_vs_female_pool: brain

source_name: mouse311, brain


title: mouse310_vs_female_pool: brain

source_name: mouse310, brain


title: mouse318_vs_female_pool: brain

source_name: mouse318, brain


title: mouse312_vs_female_pool: brain

source_name: mouse312, brain


title: mouse309_vs_female_pool: brain

source_name: mouse309, brain


title: mouse305_vs_female_pool: brain

source_name: mouse305, brain


title: mouse319_vs_female_pool: brain

source_name: mouse319, brain


title: mouse118_vs_female_pool: muscle

source_name: mouse118, muscle


title: mouse306_vs_female_pool: brain

source_name: mouse306, brain


title: mouse321_vs_female_pool: brain

source_name: mouse321, brain


title: mouse320_vs_female_pool: brain

source_name: mouse320, brain


title: mouse314_vs_female_pool: brain

source_name: mouse314, brain


title: mouse303_vs_female_pool: brain

source_name: mouse303, brain

source_name: reference pool (female, brain)


title: mouse308_vs_female_pool: brain

source_name: mouse308, brain


title: mouse313_vs_female_pool: brain

source_name: mouse313, brain


title: mouse307_vs_female_pool: brain

source_name: mouse307, brain


title: mouse304_vs_female_pool: brain

source_name: mouse304, brain


title: mouse300_vs_female_pool: brain

source_name: mouse300, brain


title: mouse299_vs_female_pool: brain

source_name: mouse299, brain


title: mouse302_vs_female_pool: brain

source_name: mouse302, brain


title: mouse296_vs_female_pool: brain

source_name: mouse296, brain


title: mouse294_vs_female_pool: brain

source_name: mouse294, brain


title: mouse291_vs_female_pool: brain

source_name: mouse291, brain


title: mouse301_vs_female_pool: brain

source_name: mouse301, brain


title: mouse298_vs_female_pool: brain

source_name: mouse298, brain


title: mouse289_vs_female_pool: brain

source_name: mouse289, brain


title: mouse297_vs_female_pool: brain

source_name: mouse297, brain


title: mouse286_vs_female_pool: brain

source_name: mouse286, brain


title: mouse288_vs_female_pool: brain

source_name: mouse288, brain


title: mouse292_vs_female_pool: brain

source_name: mouse292, brain

source_name: reference pool (female, brain)


title: mouse284_vs_female_pool: brain

source_name: mouse284, brain


title: mouse293_vs_female_pool: brain

source_name: mouse293, brain


title: mouse295_vs_female_pool: brain

source_name: mouse295, brain


title: mouse287_vs_female_pool: brain

source_name: mouse287, brain


title: mouse282_vs_female_pool: brain

source_name: mouse282, brain


title: mouse281_vs_female_pool: brain

source_name: mouse281, brain


title: mouse285_vs_female_pool: brain

source_name: mouse285, brain


title: mouse279_vs_female_pool: brain

source_name: mouse279, brain


title: mouse283_vs_female_pool: brain

source_name: mouse283, brain


title: mouse280_vs_female_pool: brain

source_name: mouse280, brain


title: mouse277_vs_female_pool: brain

source_name: mouse277, brain


title: mouse290_vs_female_pool: brain

source_name: mouse290, brain


title: mouse276_vs_female_pool: brain

source_name: mouse276, brain


title: mouse269_vs_female_pool: brain

source_name: mouse269, brain


title: mouse273_vs_female_pool: brain

source_name: mouse273, brain


title: mouse272_vs_female_pool: brain

source_name: mouse272, brain


title: mouse278_vs_female_pool: brain

source_name: mouse278, brain

source_name: reference pool (female, brain)


title: mouse271_vs_female_pool: brain

source_name: mouse271, brain


title: mouse267_vs_female_pool: brain

source_name: mouse267, brain


title: mouse266_vs_female_pool: brain

source_name: mouse266, brain


title: mouse265_vs_female_pool: brain

source_name: mouse265, brain


title: mouse262_vs_female_pool: brain

source_name: mouse262, brain


title: mouse275_vs_female_pool: brain

source_name: mouse275, brain


title: mouse263_vs_female_pool: brain

source_name: mouse263, brain


title: mouse264_vs_female_pool: brain

source_name: mouse264, brain


title: mouse274_vs_female_pool: brain

source_name: mouse274, brain


title: mouse268_vs_female_pool: brain

source_name: mouse268, brain


title: mouse259_vs_female_pool: brain

source_name: mouse259, brain


title: mouse270_vs_female_pool: brain

source_name: mouse270, brain


title: mouse258_vs_female_pool: brain

source_name: mouse258, brain


title: mouse254_vs_female_pool: brain

source_name: mouse254, brain


title: mouse261_vs_female_pool: brain

source_name: mouse261, brain


title: mouse253_vs_female_pool: brain

source_name: mouse253, brain


title: mouse249_vs_female_pool: brain

source_name: mouse249, brain

source_name: reference pool (female, brain)


title: mouse260_vs_female_pool: brain

source_name: mouse260, brain


title: mouse255_vs_female_pool: brain

source_name: mouse255, brain


title: mouse257_vs_female_pool: brain

source_name: mouse257, brain


title: mouse252_vs_female_pool: brain

source_name: mouse252, brain


title: Trichophyton erinacei_genome_rep3

status: Public on May 04 2010

type: genomic

city: Beijing

first: Qi

last: Jin

state: Beijing

address: No.6 Rongjing East Street, BDA

country: China

institute: National Institute for Viral Disease Control and Prevention

description: no

hyb_protocol: The two-color labeled DNA were mixed and combined with 5μg human Cot1 and 2μg polyA, then dried to 10μl final volume. The 10μl two-labeled target DNA preparations were combined with 1.5μl 50×Denhardts,2.25ul 20×SSC,1.125μl yeast tRNA (25μg/μl),0.375μl 1M HEPES（pH 7.0）and 0.375μl 10% SDS. This hybridization mixture was incubated for 2 min at 100℃,and the total volume was applied to the microarray slides. The sildes were sealed in hybridization chambers and left overnight at 65℃.Followed hybridization, the slides were washed for 5min in 2×SSC,0.1%(w/v)SDS twice,5min 1×SSC twice, and 5min in 0.2×SSC twice before being spun dry and scanned with Axon GenePix 4100A scanner(Axon Instruments).

scan_protocol: The slides was scanned with Axon GenePix 4100A scanner(Axon Instruments). The raw data were produced and normlized by GenePix Pro 5.0 software.

data_processing: Signal intensities were background corrected then the background intensity was subtracted locally. To be included in further normlization analysis, spots had to have (1) a signal intensity 55% of which was greater than 2* the standard deviation of the median background signal, and (2) a SNR532 (signal-noise ratio) of>= 3. The normlization method was Ratio Of Medians of all Features equal to 1.

molecule: genomic DNA

organism: Trichophyton benhamiae

source_name: Trichophyton erinacei ATCC-28446

label_protocol: Genomic DNA were isolated from  YEPD cultures by using Plant DNA Extract Kit (Qiagen). 4ug genomic DNA were labeled by DNA Labeling Kit (Invitrogen). Test strains and labeled by Cy5-dCTP. Modification included 3μl Cy5-dCTP (Amersham) were used for each 50 μl labeling reaction. DNA were purified with the Qiaquick PCR Purification Kit (Qiagen).

growth_protocol: Trichophyton erinacei were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

extract_protocol: Genomic DNA was prepared using the Plant DNA Extraction kit (Qiagen) according to manufacturer instructions.

tag: Trichophyton erinacei ATCC-28446 Genomic DNA

organism: Trichophyton rubrum

source_name: Trichophyton rubrum BMU01672

label_protocol: Genomic DNA were isolated from YEPD cultures by using Plant DNA Extract Kit (Qiagen). 4ug genomic DNA were labeled by DNA Labeling Kit (Invitrogen). T. rubrum BMU01672 was the reference strain and was labeled by Cy3-dCTP. Modification included 3μl Cy3-dCTP (Amersham) were used for each 50 μl labeling reaction.

growth_protocol: Trichophyton rubrum were cultured in liquid Yeast Extract Peptone Dextrose[YPED] media at 26℃.

tag: Trichophyton rubrum BMU01672 genomic DNA


title: mouse250_vs_female_pool: brain

source_name: mouse250, brain


title: mouse248_vs_female_pool: brain

source_name: mouse248, brain


title: mouse245_vs_female_pool: brain

source_name: mouse245, brain


title: mouse243_vs_female_pool: brain

source_name: mouse243, brain


title: mouse256_vs_female_pool: brain

source_name: mouse256, brain


title: mouse251_vs_female_pool: brain

source_name: mouse251, brain


title: mouse247_vs_female_pool: brain

source_name: mouse247, brain


title: mouse246_vs_female_pool: brain

source_name: mouse246, brain


title: mouse240_vs_female_pool: brain

source_name: mouse240, brain


title: mouse233_vs_female_pool: brain

source_name: mouse233, brain


title: mouse241_vs_female_pool: brain

source_name: mouse241, brain

source_name: reference pool (female, brain)


title: mouse237_vs_female_pool: brain

source_name: mouse237, brain


title: mouse238_vs_female_pool: brain

source_name: mouse238, brain


title: mouse236_vs_female_pool: brain

source_name: mouse236, brain


title: mouse235_vs_female_pool: brain

source_name: mouse235, brain


title: mouse232_vs_female_pool: brain

source_name: mouse232, brain


title: mouse239_vs_female_pool: brain

source_name: mouse239, brain


title: mouse234_vs_female_pool: brain

source_name: mouse234, brain


title: mouse244_vs_female_pool: brain

source_name: mouse244, brain


title: mouse228_vs_female_pool: brain

source_name: mouse228, brain


title: mouse223_vs_female_pool: brain

source_name: mouse223, brain


title: mouse224_vs_female_pool: brain

source_name: mouse224, brain


title: mouse227_vs_female_pool: brain

source_name: mouse227, brain


title: mouse231_vs_female_pool: brain

source_name: mouse231, brain


title: mouse229_vs_female_pool: brain

source_name: mouse229, brain


title: mouse219_vs_female_pool: brain

source_name: mouse219, brain


title: mouse230_vs_female_pool: brain

source_name: mouse230, brain


title: mouse217_vs_female_pool: brain

source_name: mouse217, brain

source_name: reference pool (female, brain)


title: mouse216_vs_female_pool: brain

source_name: mouse216, brain


title: mouse211_vs_female_pool: brain

source_name: mouse211, brain


title: mouse222_vs_female_pool: brain

source_name: mouse222, brain


title: mouse218_vs_female_pool: brain

source_name: mouse218, brain


title: mouse213_vs_female_pool: brain

source_name: mouse213, brain


title: mouse212_vs_female_pool: brain

source_name: mouse212, brain


title: mouse220_vs_female_pool: brain

source_name: mouse220, brain


title: mouse221_vs_female_pool: brain

source_name: mouse221, brain


title: mouse214_vs_female_pool: brain

source_name: mouse214, brain


title: mouse226_vs_female_pool: brain

source_name: mouse226, brain


title: mouse215_vs_female_pool: brain

source_name: mouse215, brain


title: mouse210_vs_female_pool: brain

source_name: mouse210, brain


title: mouse208_vs_female_pool: brain

source_name: mouse208, brain


title: mouse207_vs_female_pool: brain

source_name: mouse207, brain


title: mouse209_vs_female_pool: brain

source_name: mouse209, brain


title: mouse205_vs_female_pool: brain

source_name: mouse205, brain


title: mouse203_vs_female_pool: brain

source_name: mouse203, brain

source_name: reference pool (female, brain)


title: mouse204_vs_female_pool: brain

source_name: mouse204, brain


title: mouse206_vs_female_pool: brain

source_name: mouse206, brain


title: mouse197_vs_female_pool: brain

source_name: mouse197, brain


title: mouse196_vs_female_pool: brain

source_name: mouse196, brain


title: mouse195_vs_female_pool: brain

source_name: mouse195, brain


title: mouse202_vs_female_pool: brain

source_name: mouse202, brain


title: mouse198_vs_female_pool: brain

source_name: mouse198, brain


title: mouse201_vs_female_pool: brain

source_name: mouse201, brain


title: mouse192_vs_female_pool: brain

source_name: mouse192, brain


title: mouse199_vs_female_pool: brain

source_name: mouse199, brain


title: mouse186_vs_female_pool: brain

source_name: mouse186, brain


title: mouse191_vs_female_pool: brain

source_name: mouse191, brain


title: mouse185_vs_female_pool: brain

source_name: mouse185, brain


title: mouse193_vs_female_pool: brain

source_name: mouse193, brain


title: mouse189_vs_female_pool: brain

source_name: mouse189, brain


title: mouse184_vs_female_pool: brain

source_name: mouse184, brain


title: mouse187_vs_female_pool: brain

source_name: mouse187, brain

source_name: reference pool (female, brain)


title: mouse181_vs_female_pool: brain

source_name: mouse181, brain


title: mouse194_vs_female_pool: brain

source_name: mouse194, brain


title: mouse183_vs_female_pool: brain

source_name: mouse183, brain


title: mouse188_vs_female_pool: brain

source_name: mouse188, brain


title: mouse182_vs_female_pool: brain

source_name: mouse182, brain


title: Allogeneic tumor-activated Treg_biological_rep5

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

country: USA

institute: Washington University School of Medicine

description: Ascites fluid of knock-in mice (H-2b) challenged for 5 days with an intraperitoneal dose of 1e6 P815 mastocytoma cells.

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: MAS5 (data corrected to 1500 Baseline).

label: biotin

molecule: total RNA

source_name: allogeneic tumor-activated Treg cells

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Foxp3-ires-GFP knock-in mice were derived in the 129/SvJ background (H-2b).

extract_protocol: RNA was extracted using Trizol.

treatment_protocol: Naive CD4+Foxp3+ Treg cells were purified from the resting spleens of Foxp3-ires-GFP knock-in mice derived in the 129/SvJ background.  Allogeneic tumor-activated Treg cells were FACS-purifed from the ascites fluid of knock-in mice (H-2b) that had been challenged for 5 days with an intraperitoneal dose of 1e6 P815 mastocytoma cells (originally derived from DBA/2 mice; H-2d).  GVHD-activated Treg cells were purified from lethally irradiated (900 cGy) Balb/c mice (H-2d) that had been transplanted intravenously with 2e6 129/SvJ WT bone marrow cells and 2e6 MACS-purified CD4+ and CD8+ T cells harvested from 129/SvJ Foxp3-ires-GFP knock-in mice.  GVHD-activated Treg cells were FACS-purifed on day 4 post-transplant.  Sort purity was routinely >95%.

value: ascites fluid

tag: cell type

value: Allogeneic tumor-activated Treg cells


title: Allogeneic tumor-activated Treg_biological_rep3


title: GVHD-activated Treg_biological_rep2

description: Spleens of lethally irradiated WT Balb/c recipients of 2e6 T cells from 129/SvJ Foxp3-ires-GFP knock-in mice and 2e6 bone marrow cells from 129/SvJ WT mice (4 days post-transplant)

source_name: GVHD-activated Treg cells

value: BALB/c

value: spleen

value: GVHD-activated Treg cells


title: Naïve Treg_biological_rep4

description: Resting spleens of Foxp3-ires-GFP knock-in mice

source_name: Naive CD4+Foxp3+ Treg cells

value: Naive CD4+Foxp3+ Treg cells


title: Naïve Treg_biological_rep5


title: GVHD-activated Treg_biological_rep3


title: Allogeneic tumor-activated Treg_biological_rep1


title: Allogeneic tumor-activated Treg_biological_rep4


title: Allogeneic tumor-activated Treg_biological_rep2


title: Murine 3T3 L1 cells, DMSO, 48h, biological repl #3

status: Public on Aug 30 2009

city: Research Triangle Park

first: James

last: Rong

state: NC

address: 5 Moore Drive

institute: GlaxoSmithKline

description: Biological replicate 3 of 3.

hyb_protocol: The biotinylated cRNA were randomized again to avoid batch effects. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150. Probe sets with intensity values >= 19.9, representing the 95 percentile of the built-in Affymetrix negative control probe sets for all the chips, were considered present.

label: Biotin

source_name: 3T3 L1, DMSO, 48h

label_protocol: To avoid batch effects, RNA samples were randomized. Biotinylated cRNA were prepared from the RNA samples (5 microgram of total RNA) according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For adipocyte differentiation, C3H/10T1/2 cells were plated at 1.26 x 105 cells/cm2 and allowed to grow 24 hrs to reach confluence. Cells were then differentiated in DMEM/F12 (Invitrogen) containing RSG, (10 μM) and insulin (1 μM) for 6 days. 3T3 L1 cells were plated at 63,000 cells/cm2 and allowed to grow 3 days to reach confluence. The cells were then incubated with complete medium containing insulin (Invitrogen; 0.8 μM), 3-isobutyl-1-methylxanthine (Sigma; 0.5 mM), dexamethasone (Sigma; 0.25 μM), and RSG, (GlaxoSmithKline, Research Triangle Park, NC, 100 nM) for 2 days, followed by complete medium containing insulin (0.8 mM) for 2 days, and complete medium alone for 3 more days.

extract_protocol: Qiagen RNeasy mini kit was used following the manufacturer's instructions.

treatment_protocol: Differentiated C3H/10T1/2 and 3T3 L1 adipocytes were incubated for 24 hrs in a wash-out medium, i.e., DMEM/F12 medium containing 1% essential fatty acid-free bovine serum albumin (BSA, Sigma), and harvested directly (0hr) or after treatment in the wash-out medium with RSG, (1 microM) or DMSO for 1, 2, 4, 7, 24 and 48 hrs.

value: differentiated adipocytes


title: Naïve Treg_biological_rep6


title: Murine 3T3 L1 cells, DMSO, 24h, biological repl #3

description: Biological replicate 3 of 3.

source_name: 3T3 L1, DMSO, 24h


title: Murine 3T3 L1 cells, DMSO, 48h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, DMSO, 48h, biological repl #1

description: Biological replicate 1 of 3.


title: GVHD-activated Treg_biological_rep1


title: Murine 3T3 L1 cells, DMSO, 7h, biological repl #1

description: Biological replicate 1 of 3.

source_name: 3T3 L1, DMSO, 7h


title: Murine 3T3 L1 cells, DMSO, 24h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, DMSO, 24h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, DMSO, 7h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, DMSO, 7h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, DMSO, 4h, biological repl #2

description: Biological replicate 2 of 3.

source_name: 3T3 L1, DMSO, 4h


title: Murine 3T3 L1 cells, DMSO, 4h, biological repl #3

description: Biological replicate 3 of 3.


title: mouse242_vs_female_pool: brain

source_name: mouse242, brain


title: Murine 3T3 L1 cells, DMSO, 4h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, DMSO, 2h, biological repl #2

description: Biological replicate 1 of 2.

source_name: 3T3 L1, DMSO, 2h


title: Murine 3T3 L1 cells, DMSO, 1h, biological repl #3

description: Biological replicate 3 of 3.

source_name: 3T3 L1, DMSO, 1h


title: Murine 3T3 L1 cells, DMSO, 1h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 24h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, DMSO, 1h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, DMSO, 2h, biological repl #3

description: Biological replicate 2 of 2.


title: Murine C3H10T1/2 cells, DMSO, 24h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 48h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, DMSO, 24h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, DMSO, 48h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 7h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, DMSO, 2h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, DMSO, 4h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, DMSO, 1h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, DMSO, 7h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 7h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, DMSO, 48h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, DMSO, 4h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 2h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, DMSO, 2h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 1h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, DMSO, 4h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, DMSO, 1h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, RSG, 48h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, RSG, 24h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, RSG, 7h, biological repl #1

description: Biological replicate 1 of 3.

source_name: 3T3 L1, RSG, 7h


title: Murine 3T3 L1 cells, RSG, 24h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, RSG, 24h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, RSG, 7h, biological repl #2

description: Biological replicate 2 of 3.


title: mouse190_vs_female_pool: brain

source_name: mouse190, brain

source_name: reference pool (female, brain)


title: Murine 3T3 L1 cells, RSG, 48h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, RSG, 7h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, RSG, 48h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, RSG, 4h, biological repl #3

description: Biological replicate 3 of 3.

source_name: 3T3 L1, RSG, 4h


title: Murine 3T3 L1 cells, RSG, 4h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, RSG, 2h, biological repl #1

description: Biological replicate 1 of 3.

source_name: 3T3 L1, RSG, 2h


title: Murine 3T3 L1 cells, RSG, 2h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 48h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine 3T3 L1 cells, RSG, 1h, biological repl #3

description: Biological replicate 3 of 3.

source_name: 3T3 L1, RSG, 1h


title: Murine 3T3 L1 cells, RSG, 2h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, RSG, 4h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine 3T3 L1 cells, RSG, 1h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine 3T3 L1 cells, RSG, 1h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 48h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 24h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 48h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 24h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 24h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 7h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 7h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 4h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 4h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 4h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 2h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 1h, biological repl #2

description: Biological replicate 2 of 3.


title: Murine C3H10T1/2 cells, RSG, 7h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 1h, biological repl #3

description: Biological replicate 3 of 3.


title: Murine C3H10T1/2 cells, RSG, 2h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 1h, biological repl #1

description: Biological replicate 1 of 3.


title: Murine C3H10T1/2 cells, RSG, 2h, biological repl #2

description: Biological replicate 2 of 3.


title: Mock - 24hr; 17_24R2

status: Public on Aug 01 2009

city: Edinburgh

first: Paul

middle: A

last: Lacaze

address: 49 Little France Crescent

department: School of Medicine

country: United Kingdom

institute: University of Edinburgh

description: Transfection of murine bone-marrow derived macrophages (BMDMs) with non-targeting (control) siRNA and 11 sequence-specific siRNAs was performed using a cationic lipid transfection reagent (Lipofectamine2000) prior to stimulation with IFNγ. Total RNA was harvested from cells and gene expression measured on Affymetrix GeneChip Mouse Exon 1.0 ST Arrays.

hyb_protocol: Hybridization according to Affymetrix Mouse Exon Array 1.0ST protocol (Affymetrix, Santa Clara, US)

scan_protocol: Affymetrix Genechip 7G ScanMachinePrt1

data_processing: RMA normalization using "core" set of probes

source_name: BMDMs, Mock transfections - Lipofectamine2000 & non-targeting siRNA treatment

label_protocol: Microarray target labelling: 150 ng of total RNA was processed using the Exon array target labelling kit (Affymetrix, Santa Clara, US) according to manufacturer’s instructions for small sample labelling without the use of the RiboMinus step.

growth_protocol: Balb/c male mice age 10-12 weeks. Bone marrow (containing primary mouse monocytes) was flushed from femurs and differentiated for 7 days in DMEM-F12/10% FCS/10% L929 medium (releasing CSF-1). Cells grown in 24-well plates at a seeding density of 5x105 cells/well. Media changes on days 3 and 5.

extract_protocol: Total RNA was extracted using an RNeasy Plus kit (Qiagen) according to manufacturer's instructions. RNA was quantified and quality controlled using a NanoDrop spectrophotometer (NanoDrop Technologies) and BioAnalyser 2100 (Agilent). They were then washed and scanned according to manufacturer's recommendations

treatment_protocol: Transfection of siRNA and IFNγ treatment  Differentiated primary macrophages were subject to siRNAs SMARTpools (Thermo Fisher Inc) designed to each mRNA target (4 siRNAs per pool). siRNAs were purchased at a 5 nmol scale and redissolved in 1x siRNA buffer (Thermo Fisher Inc) to a final concentration of 1 µM. To transfect at a final concentration of 20 nM, 1 µl of siRNA SMARTpool was used with 49 µl of Optimem (Invitrogen, CA, USA) solution while 2 µl of Lipofectamine 2000 (L2K, Invitrogen) was mixed with 48 µl Optimem. Following incubation for 5 min, the siRNA mix was added to the L2K mix and incubated for a further 30 min, after which 400 µl of DMEM-F12/10% FCS/L929 medium lacking antibiotics was added to the siRNA:L2K complexes. Growth medium was removed and cells were washed 1x in PBS before 500 µl of the siRNA:L2K liposomes were added. Cells were then incubated for a further 24 h (37ºC, 5% CO2). For IFNγ treatments, growth medium was replaced with medium containing 10 U/ml recombinant mouse IFNγ. Cells were incubated for 24 h prior to harvesting of total RNA.


title: Mock - 24hr; 18_24R3

tag: Balb/c male mice age 10-12 weeks. Bone marrow (containing primary mouse monocytes) was flushed from femurs and differentiated for 7 days in DMEM-F12/10% FCS/10% L929 medium (releasing CSF-1). Cells grown in 24-well plates at a seeding density of 5x105 cells/well. Media changes on days 3 and 5.


title: Mock - 24hr; 12_24C3


title: Mock - 24hr; 16_24R1


title: Mock - 24hr; 14_24L2


title: Mock - 24hr; 13_24L1


title: Mock - 24hr; 11_24C2


title: Mock - 24hr; 10_24C1


title: B6-mMSCs-p28

status: Public on Aug 13 2009

city: Leiden

first: Alex

middle: B

last: Mohseny

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: The mm8 murine Genome Build (Feb 2006) from NCBI’s Genebank was used to allocate probes.

hyb_protocol: After mixing experimental and reference labelled DNA, Cot-1 DNA (Invitrogen), blocking agent and hybridization buffer (Agilent) were added. Samples were applied to the high resolution 244K arrays and hybridized at 65 ºC at 20 rotations per minute in a hybridization oven (Affymetrix). After 40 hours of hybridization the arrays were washed (according to the Agilent protocol).

scan_protocol: Agilent G2565BA microarray scanner was used to scan the slides right after washing.

data_processing: All data were extracted using Feature Extraction software, quality was assessed using Quality Metrics and QC Chart Tool and aberrations were studied using CGH analytics software (all provided by Agilent). Statistical analyses were performed as described previously (Selvarajah et al., 2007).

source_name: Normal spleen.

label_protocol: 3 µg of genomic DNA was digested with AluI and RsaI restriction enzymes (Promega). Digestion quality was checked by running 2µl of digested DNA on a 0.8% agarose gel, DNA fragment-size between 200 and 500 bp was considered as appropriate digestion. Subsequently sample was labelled with Cy5-dUTP. Labelled samples were purified by using a Microcon YM-30 filter (Millipore Corporation) after which expected yield and specific dye activity of the samples were measured using NanoDrop.

growth_protocol: Cells were cultured in medium consisting of α-minimal essential medium (α-MEM; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 2% penicillin/streptomycin (P/S, Invitrogen Corporation) and 2% L-glutamine (Invitrogen Corporation) on uncoated polystyrene dishes at 37°C with 5% CO2. When reaching 80% confluence, part of the cells was collected for DNA and RNA isolation and the rest was passaged.

extract_protocol: Genomic DNA was extracted and purified using a Wizard Genomic DNA Purification Kit (Promega). DNA concentration and purity was measured for each sample using a NanoDrop spectrophotometer (Isogen) according to the manufacturer’s manual. Samples were prepared further as described previously (Selvarajah et al., 2007).

tag: Normal spleen DNA from C57BL/6 female mice.

source_name: murine MSCs

label_protocol: 3 µg of genomic DNA was digested with AluI and RsaI restriction enzymes (Promega). Digestion quality was checked by running 2µl of digested DNA on a 0.8% agarose gel, DNA fragment-size between 200 and 500 bp was considered as appropriate digestion. Subsequently sample was labelled with Cy3-dUTP. Labelled samples were purified by using a Microcon YM-30 filter (Millipore Corporation) after which expected yield and specific dye activity of the samples were measured using NanoDrop.

tag: Murine mesenchymal stem cells derived from C57BL/6 bone marrow and cultured in vitro for 28 passages.


title: Mock - 5hr; 6_5L3


title: Mock - 24hr; 15_24L3


title: Mock - 5hr; 8_5R2


title: Bc-mMSCs-p28

tag: Normal spleen DNA from BALB/c female mice.

source_name: MSCs DNA Bc p28

tag: Murine mesenchymal stem cells derived from BALB/c bone marrow and cultured in vitro for 12 passages.


title: TmMSCs

source_name: normal spleen

source_name: Transformed murine mesenchymal stem cells (TmMSCs)

tag: Murine mesenchymal stem cells which are transformed after long term in vitro passaging in a way they form tumours upon injection into nude mice.


title: Mock - 5hr; 4_5L1


title: Mock - 5hr; 7_5R1


title: Mock - 5hr; 9_5R3


title: Mock - 5hr; 3_5C3


title: Mock - 5hr; 1_5C1


title: Mock - 5hr; 2_5C2


title: B6-mMSCs-p12

source_name: Bone marrow murine MSCs

tag: Murine mesenchymal stem cells derived from C57BL/6 bone marrow and cultured in vitro for 12 passages.


title: RT2

source_name: Tumour cells RT2.

tag: Osteosarcoma-like tumour cells isolated from tumours formed in mice after injecting them the T1 cells (in vivo second passage).


title: T1

source_name: Tumour cells T1

tag: Osteosarcoma-like tumour cells isolated from tumours formed in mice after injecting them TmMSCs.


title: Bc-mMSCs-p12

source_name: MSCs Bc p12


title: Traf1_IFN-_A21B TF_RNAi-EXON_180407

source_name: BMDMs, IFNg stimulation, siRNA treatment


title: Traf1_IFN+_B21B TF_RNAi-EXON_180407


title: Traf1_IFN-_A21C TF_RNAi-EXON_180407


title: Traf1_IFN+_B21A TF_RNAi-EXON_180407


title: Stat2_IFN+_B14C TF_RNAi-EXON_210307


title: Traf1_IFN-_A21A TF_RNAi-EXON_180407


title: Traf1_IFN+_B21D TF_RNAi-EXON_180407


title: Stat2_IFN-_A14C TF_RNAi-EXON_210307


title: Stat2_IFN-_A14B TF_RNAi-EXON_210307


title: Stat2_IFN+_B14A TF_RNAi-EXON_210307


title: Stat2_IFN+_B14B TF_RNAi-EXON_210307


title: Stat1_IFN+_B13C TF_RNAi-EXON_020107


title: Stat2_IFN-_A14A TF_RNAi-EXON_210307


title: Stat1_IFN-_A13B TF_RNAi-EXON_020107


title: Stat1_IFN-_A13C TF_RNAi-EXON_020107


title: Stat1_IFN+_B13B TF_RNAi-EXON_020107


title: Stat1_IFN-_A13A TF_RNAi-EXON_020107


title: SOD2_IFN+_B31A TF_RNAi-EXON_210307


title: Stat1_IFN+_B13A TF_RNAi-EXON_020107


title: SOD2_IFN-_A31C TF_RNAi-EXON_210307


title: SOD2_IFN+_B31B TF_RNAi-EXON_210307


title: SOD2_IFN+_B31C TF_RNAi-EXON_210307


title: SOD2_IFN-_A31B TF_RNAi-EXON_210307


title: SOD2_IFN-_A31A TF_RNAi-EXON_210307


title: Riscfree_IFN+_CON3C TF_RNAi-EXON_130207


title: Nfkb2_IFN+_B16A TF_RNAi-EXON_020107


title: Nfkb2_IFN+_B16C TF_RNAi-EXON_020107


title: Riscfree_IFN-_CON5D TF_RNAi-EXON_130207


title: Riscfree_IFN-_CON5C TF_RNAi-EXON_130207


title: Nfkb2_IFN+_B16B TF_RNAi-EXON_020107


title: Riscfree_IFN+_CON3B TF_RNAi-EXON_130207


title: Nfkb2_IFN-_A16C TF_RNAi-EXON_020107


title: Mock - 5hr; 5_5L2


title: Lyn_IFN+_B25B TF_RNAi-EXON_151206


title: Nfkb2_IFN-_A16B TF_RNAi-EXON_020107


title: Riscfree_IFN+_CON3A TF_RNAi-EXON_130207


title: Lyn_IFN-_A25C TF_RNAi-EXON_190407


title: Nfkb2_IFN-_A16A TF_RNAi-EXON_020107


title: Irf5_IFN+_B12C TF_RNAi-EXON_220307


title: Lyn_IFN+_B25C TF_RNAi-EXON_190407


title: Lyn_IFN-_A25B TF_RNAi-EXON_190407


title: UMARY-1209-TCTX-CpG

status: Public on Apr 20 2010

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Human Brain Tissue: TCTX

hyb_protocol: Two bead types correspond to each CpG locus, one to the methylated (C) state, and the other to the unmethylated (T) state. After extension, the BeadChip was fluorescently stained.

scan_protocol: Illumina Beadstation BeadArray laser confocal scanner to measure the intensities of unmethylated and methylated bead types for each locus.

data_processing: Beadstudio Methylation Module v3.2.0, no normalization (analysis performed on the non-normalized data).

label: C-Bio and A-DNP

organism: Homo sapiens

source_name: Human Brain Tissue: TCTX

label_protocol: 1ug of genomic DNA underwent bisulfite conversion using the WZ-96 DNA Methylation Kit according to the manufacturer’s protocol (Zymo Research Corp, Orange, CA). Incubation conditions used during conversion were as follows: (95°C for 30 seconds, 50°C for 1 hour) for 16 cycles, hold overnight at 4°C. Unmethylated cytosines were chemically deaminated to uracil in the presence of bisulfite, while methylated cytosines were refractory to the effects of bisulfite and remained as cytosines. Methylation was then detected as a C/T nucleotide polymorphism at each CpG site. After bisulfite conversion, each sample was whole-genome amplified, fragmented, and hybridized to the BeadChip. DNA molecules anneal to locus-specific DNA oligomers.

extract_protocol: Genomic DNA for the Infinium methylation assay was extracted using phenol-chloroform and ethanol precipitation. DNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and DNA extraction was repeated using a new tissue aliquot for samples with DNA concentration less than 50ng/ul, or with a 260/280 ratio less than 1.7.

tag: gender

tag: age

tag: pmi

tag: tissuebank

value: UMARY

value: temporal cortex


title: Irf5_IFN-_A12B TF_RNAi-EXON_220307


title: Lyn_IFN-_A25A TF_RNAi-EXON_190407


title: Lyn_IFN+_B25B TF_RNAi-EXON_190407


title: Irf5_IFN-_A12C TF_RNAi-EXON_220307


title: Irf5_IFN+_B12B TF_RNAi-EXON_220307


title: Irf3_IFN-_A11C TF_RNAi-EXON_160407


title: Irf3_IFN-_A11B TF_RNAi-EXON_160407


title: Irf5_IFN+_B12A TF_RNAi-EXON_220307


title: IRF3_IFN+_B11A TF_RNAi-EXON_160407


title: IRF3_IFN+_B11C TF_RNAi-EXON_160407


title: IfnB_IFN+_B15B TF_RNAi-EXON_160407


title: Irf5_IFN-_A12A TF_RNAi-EXON_220307


title: IfnB_IFN+_B15A TF_RNAi-EXON_160407


title: Irf3_IFN-_A11A TF_RNAi-EXON_160407


title: IRF3_IFN+_B11B TF_RNAi-EXON_160407


title: IfnB_IFN-_A15C TF_RNAi-EXON_160407


title: Ifi47_IFN-_A33C TF_RNAi-EXON_190407


title: IfnB_IFN-_A15A TF_RNAi-EXON_160407


title: IfnB_IFN-_A15B TF_RNAi-EXON_160407


title: IfnB_IFN+_B15C TF_RNAi-EXON_160407


title: Ifi47_IFN+_B33A TF_RNAi-EXON_190407


title: Ifi47_IFN+_B33B TF_RNAi-EXON_190407


title: Ifi47_IFN+_B33C TF_RNAi-EXON_190407


title: Ifi47_IFN-_A33B TF_RNAi-EXON_190407


title: Casp4_IFN+_B23B TF_RNAi-EXON_180407


title: Casp4_IFN+_B23C TF_RNAi-EXON_180407


title: Liver_Epicatechin_2

city: Davis

first: eskouhie

middle: Hagop

last: Tchaparian

state: CA

address: UC Davis, One Shields Ave

department: Nutrition

institute: University of Ca, Davis

description: Pooled liver RNA from 6 rats fed with epicatechin (Epi) added at 1000 mg Epi/kg to amino acid semi-purified based diet (ASD)

hyb_protocol: Hybridization was performed using the CodeLink Expression Assay Reagent Kit and following the standard procedure for the Codelink Array Bioassays.

scan_protocol: Scanning and image analyses were performed with Axon’s 4000B using CodeLink’s Expression Analysis software.

data_processing: Data exported from the CodeLink analysis software was normalized using global Loess normalization where signal intensities from each array are Loess normalized to the average intensity of all arrays after removing high variance data points.  Data from the individual single-dye experimental and reference arrays were combined and intensity values averaged and compared within and between groups to generate gene expression ratios along with t-test p-values and intensity-based ratio Z-scores.  Clustering of the data was performed with a partitioning algorithm substantially similar to the CAST algorithm (34), but with a dynamically chosen threshold set to the 15th percentile value of 500 randomly chosen gene expression distances.  These gene expression distances were calculated as cosine angle distances between the gene expression fold change vectors.

organism: Rattus norvegicus

source_name: liver

label_protocol: Labeling was performed using standard procedures and instructions for the Codelink® Array Bioassays. The biotin-labeled cRNA target was prepared by a linear amplification method. The poly(A)+ RNA subpopulation (within the total RNA population) was primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5′ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT was performed in the presence of biotinylated nucleotides to label the target cRNA.

extract_protocol: Total RNA was isolated from the liver of each rat using Trizol reagent (Invitrogen, Carlsbad, CA) and further purified using Qiagen RNA mini-kits (Qiagen, Valencia, CA). On-column DNA digestion using RNAse Free DNAase kit (Qiagen, Valencia, CA) was performed to remove DNA residues.

treatment_protocol: Rats were fed an amino acid semi-purified based diet (ASD), which provided all known required nutrients in sufficient quantities to provide maximal growth, reproduction, and lactation.   The ASD contained < 5 fmol PQQ/g. To assess the response to PQQ, male Sprague-Dawley rats, (Charles River Laboratory, Inc., Wilmington, MA) weighing ~250 grams (7-8 weeks old) were fed the ASD for two weeks.  Groups of rats (n = 6/group) were then challenged for an additional two weeks with PQQ added at 2.5 mg PQQ/Kg ASD.  For comparisons, separate groups (6 rats each) were fed epicatechin (Epi) added at 1000 mg Epi/kg ASD, or injected i.p. with dexamethasone (Dex, 100 mg Dex/Kg body wt), clofibrate (Clo, 100 mg Clo/Kg body wt), or phenobarbital (Pb, 80 mg Pb/Kg body wt) 3 hours prior to harvesting liver tissue .

tag: tissue

tag: treatment

value: epicatechin


title: Liver_PQQ_2

description: Pooled liver RNA from 6 rats with PQQ added at 2.5 mg PQQ/Kg to to amino acid semi-purified based diet (ASD)

value: PQQ


title: Liver_Vehicle_1

description: Pooled liver RNA from 6 rats fed with amino acid semi-purified based diet (ASD)

value: vehicle


title: Liver_PQQ_1

description: Pooled liver RNA from 6 rats fed with PQQ added at 2.5 mg PQQ/Kg to to amino acid semi-purified based diet (ASD)


title: Liver_Phenobarbital_2

description: Pooled liver RNA from 6 rats injected i.p. with phenobarbital (Pb, 80 mg Pb/Kg body wt) 3 hours prior to harvesting liver tissue

value: phenobarbital


title: Liver_Clofibrate_1

description: Pooled liver RNA from 6 rats injected i.p. with clofibrate (Clo, 100 mg Clo/Kg body wt) 3 hours prior to harvesting liver tissue

value: clofibrate


title: Casp4_IFN+_B23A TF_RNAi-EXON_151206


title: Ifi47_IFN-_A33A TF_RNAi-EXON_190407


title: Liver_Vehicle_2


title: Liver_Epicatechin_1


title: Liver_Dexamethasone_1

description: Pooled liver RNA from 6 rats injected i.p. with dexamethasone (Dex, 100 mg Dex/Kg body wt) 3 hours prior to harvesting liver tissue

value: dexamethasone


title: Liver_Dexamethasone_2


title: Liver_Phenobarbital_1


title: Casp4_IFN-_A23C TF_RNAi-EXON_180407


title: Casp4_IFN-_A23A TF_RNAi-EXON_180407


title: Casp4_IFN+_B23A TF_RNAi-EXON_180407


title: Casp4_IFN-_A23B TF_RNAi-EXON_180407


title: whole lung: TAZ-deficient mice and their littermates, TAZ-deficient

city: Tokyo

first: Akihisa

last: Mitani

address: 7-3-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: University of Tokyo

description: Microarray analysis was performed using Mouse Genome 430 2.0 Array  (Affymetrix # 900496) representing approximately 10,000 full-length genes. Sequences and GenBank accession numbers of all probe sets are available at the Affymetrix home page http://www.affymetrix.com/index.affx.

hyb_protocol: 10 µg of fragmented cRNA were hybridised (45°C, 16 hours). Hybridization was controled by use of the GeneChip® Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 400 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G. Chip analysis was performed using the Affymetrix Microarray Suite v5.0.

data_processing: GCOS/MAS5 software, Scanned Data were normalized to 100 as average.

source_name: whole lung, TAZ-deficient

label_protocol: 5 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Invitrogen).  Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf). In vitro transcription was performed on 1 µg of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNA was isolated from frozen tissue using ISOGENETM (Nippon Gene, Tokyo, Japan), according to the manufacturer's protocol.

tag: E15.5 whole lung

tag: TAZ -deficient mice and their littermates

tag: four samples were mixed for each group


title: whole lung: TAZ-deficient mice and their littermates, wildtype

source_name: whole lung, wild type

tag: E15.5 whole lungs

tag: wild type mice and their littermates


title: Liver_Clofibrate_2


title: abl DHT 16hr, biological replicate 3

status: Public on Jul 25 2009

city: Boston

first: Arjun

middle: Kumar

last: Manrai

state: MA

address: 44 Binney Street, Mail Stop LW225

department: Department of Biostatistics and Computational Biology

institute: Dana Farber Cancer Institute

description: gene expression data from prostate cancer cell lines

hyb_protocol: After fragmentation of the sample (cRNA), add hybridization mix:   150 ul 2X MES Hybridization Buffer   3 ul 10 mg/mL Herring Sperm DNA, sheared   3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3')   3 ul 50 mg/mL Acetylated BSA   15 ul 20X Eukaryotic Hybridization Controls   Adjust volume with DEPC H2O to 300 ul total volume (if  fragmentation volume is 50 ul, need 76 ul water)   -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not  frozen)  -Cool targets at 45 °C, 5 min  -Spin targets at max, 5 min  -Add 200 ul targets to each properly labeled chip  -Incubate chips at 45 °C, 60 RPM, 16-18 h  -Return the remaining volume of unused target to -20 °C  -The next day, remove target & fill chips with non-stringent buffer (A)  with no bubbles.  -Wrap chips in foil and store at 4 °C until you start fluidics.  Allow chips to equilibrate to room temperature before start fluidics and  scanning  -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.

scan_protocol: scan on Affymetrix GeneChip Scanner (GCS) 3000

data_processing: creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036

source_name: abl cellls, DHT treated for 16 hrs

label_protocol: The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).

growth_protocol: The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells  were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.

extract_protocol: RNeasy kit (Qiagen) was used to purify total RNAs.

treatment_protocol: LNCaP and abl cells  were tranfected with siAR or siControl. Abl cells  were treated with DHT (100nM) for 4 hr and 16 hr.

tag: androgen-independent prostate cancer cell line


title: abl DHT 16hr, biological replicate 2


title: abl DHT 16hr, biological replicate 1


title: abl DHT 4hr, biological replicate 3

source_name: abl cells, DHT treated for 4hrs


title: abl vehicle, biological replicate 1

source_name: abl cells, ethanol treated


title: abl siControl, biological replicate 3

source_name: abl cellls, siRNA control treated


title: abl siControl, biological replicate 2


title: abl siControl, biological replicate 1


title: LNCaP siControl, biological replicate 3

source_name: LNCaP cells, siRNA control treated

tag: androgen-dependent prostate cancer cell line


title: abl DHT 4hr, biological replicate 2


title: LNCaP siAR, biological replicate 1

source_name: LNCaP cells, siRNA against AR treated


title: LNCaP siAR, biological replicate 2


title: abl siAR, biological replicate 3

source_name: abl cells, siRNA against AR treated


title: LNCaP siControl, biological replicate 1


title: abl siAR, biological replicate 2


title: abl vehicle, biological replicate 2


title: hlh-30(tm1978)-3

status: Public on Jul 24 2009

city: Worcester

first: Marian

last: Walhout

address: 364 Plantation St - LRB#605

institute: UMASS Medical School

hyb_protocol: Fragmentation, hybridization, and wash were performed as recommended by the Affymetrix GeneChip® Expression Analysis Technical Manual

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: For the normalization and analysis of the microarray data we used R and the affy (Gautier et al., 2004), gcrma (Irizarry et al., 2006) and limma (Smyth, 2004) packages from Bioconductor (www.bioconductor.org). All microarrays for each experiment were normalized using the gcrma package. To avoid artifacts in fold-change due to very low probe intensities in both conditions, we trimmed the data keeping only probe sets that had a mean log2(signal intensity) of the three replicas of 8 or higher, in at least one condition. This threshold was chosen based on the signal intensities of the external polyA RNA and cRNA controls. The trimmed data were analyzed for differential expression using the limma package. We considered as differentially expressed those genes whose probe sets had a P < 0.01 and log2(fold-change) ≥ 0.7. Probe sets were converted to WBGene IDs using the Affymetrix annotation file “Celegans.na26.annot-trimmed.csv” and WormMart. To avoid redundancy we kept only one gene per probe set and one probe set per gene. We also removed genes encoded by the mitochondrial genome. The total number of genes detected was 6,591.

organism: Caenorhabditis elegans

source_name: hlh-30(tm1978) embryos, L1 and L2 larvae, whole animals

label_protocol: For cRNA in vitro transcription/labeling, the Enzo BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo Life Sciences) was used with overnight incubation

growth_protocol: Both wild type and mutant worms were grown on standard worm egg plates; Eggs were harvested by standard bleaching protocol, collected for embryonic RNA isolation, and plated for growing synchronous cultures of worms. L1 and L2 larval worms were collected at the appropriate time points for RNA isolation. Three biological replicates were created for each genotype and life stage and RNA from emrbyos, L1s, and L2s was pooled for each replicate

extract_protocol: RNA isolation was performed as described in Van Gilst, M et al (2005) PLoS Biol

treatment_protocol: Not applicable; grown under standard 20 degree Celsius laboratory conditions

tag: genotype

value: embryos, L1 and L2 larvae


title: abl vehicle, biological replicate 3


title: abl siAR, biological replicate 1


title: abl DHT 4hr, biological replicate 1


title: LNCaP siAR, biological replicate 3


title: hlh-30(tm1978)-1


title: CCR mutant M2 with array type maize from Affymetrix

status: Public on Jul 22 2009

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: aerial - Maize plants were grown in culture room conditions with a thermoperiod of 25 celsius day/22 celsius night and a photoperiod of 16h day/8h night. Seeds were sown in pots containing compost (H4-TREF) and fertilized one time a week with Algoflash solution. At 6-7-leaf stage samples (young piled-up internodes) were collected individually and immediatly frozen.

treatment_protocol: no treatment

tag: Zea mays, maize, corn yes - dev.stage (Boyes et al. Plant Cell 2001):7 or 8 leaves


title: N2-2

source_name: WT embryos, L1 and L2 larvae, whole animals

value: wild type


title: hlh-30(tm1978)-2


title: N2-1


title: LNCaP siControl, biological replicate 2


title: CCR mutant M1 with array type maize from Affymetrix

tag: A reverese genetic approach was performed at Biogemma on CCR gene family by use of 27500 maize lines in which an endogenous transposon 'Mutator' was been introduced. One insertional mutation was detected in CCR1 gene by usinf PCR-based approach.